GenomeAnnotation

GenomeAnnotation - Genome Annotation and Pathway Mining...

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QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. Genome Annotation and Pathway Mining BioE131
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Genome Annotation Various related (but distinct) questions: “Does genome contain [a homologue of] gene X?” (gene-by-gene) “Does genome contain [homologues of genes involved in] pathway X?” (pathway mining) “What genes are there?” (whole-genome) “What genes are being transcribed?” (experimental)
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By-gene Look for (high-scoring) alignments of protein to genome Various tools for doing this TBLASTX - translates DNA in 6 frames (limited handling of gaps) GeneWise (better handling of gaps) Exonerate - GeneWise replacement (best handling of gaps)
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How Exonerate works QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. High-scoring Segment Pairs (HSPs) Dynamic programming to fill in the gaps between HSPs Exonerate’s scoring scheme uses finite state machine theory
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QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. Finite state machines Most dynamic programming algorithms for pattern-matching or alignment can be formulated as finite-state machines E.g. the regular expression for matching the MCB binding site: /ACGCGT/ (equivalent to) /^.*ACGCGT.*$/
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Finite state machines QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. Pairwise alignment scoring schemes can also be specified as finite-state machines This one is Needleman- Wunsch:
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QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. Finite state machines Adding “padding” states to Needleman-Wunsch gives us Smith-Waterman
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QuickTimeª and a TIFF (Uncompressed) decompressor are needed to see this picture. Finite state machines Adding a state to track whether the last column used a gap gives us Gotoh Genewise and Exonerate add extra states to track frameshifts, introns, etc.
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Pathway mining Gather representative protein sequences for
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This note was uploaded on 12/03/2011 for the course BIO 118 taught by Professor Staff during the Fall '08 term at Rutgers.

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GenomeAnnotation - Genome Annotation and Pathway Mining...

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